Those studs will be difficult to get off. When I was doing the job on my ES330, the double nut method didn't work. I ended up removing the front cam sprocket and the 6 bolts holding timing cover # 3 on and rotating it about the rear cam shaft to allow the water pump to pull away from the engine. I didn't have any issues with the water-pump clearing the inner fender, seems like that's only on the RX.
I also recently did a timing belt / water pump job on my 1MZ-FE Solara. Since I was doing cam-seals, I had to take off timing cover # 3 anyways, and the water-pump cleared the inner fender.
Skip over to 7:08 in my video to watch the water pump removal:
There's a good writeup in this thread for reference: